[2023-06-29 21:39:34,087] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:39:34,089] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:39:34,089] [INFO] DQC Reference Directory: /var/lib/cwl/stg30c4be52-b8b3-4552-a7d6-7459b1ac4600/dqc_reference
[2023-06-29 21:39:35,288] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:39:35,289] [INFO] Task started: Prodigal
[2023-06-29 21:39:35,289] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e694151-943e-452c-a2fe-db1846793f87/GCA_016291815.1_ASM1629181v1_genomic.fna.gz | prodigal -d GCA_016291815.1_ASM1629181v1_genomic.fna/cds.fna -a GCA_016291815.1_ASM1629181v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:39:46,508] [INFO] Task succeeded: Prodigal
[2023-06-29 21:39:46,508] [INFO] Task started: HMMsearch
[2023-06-29 21:39:46,508] [INFO] Running command: hmmsearch --tblout GCA_016291815.1_ASM1629181v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30c4be52-b8b3-4552-a7d6-7459b1ac4600/dqc_reference/reference_markers.hmm GCA_016291815.1_ASM1629181v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:39:46,673] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:39:46,674] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5e694151-943e-452c-a2fe-db1846793f87/GCA_016291815.1_ASM1629181v1_genomic.fna.gz]
[2023-06-29 21:39:46,698] [INFO] Query marker FASTA was written to GCA_016291815.1_ASM1629181v1_genomic.fna/markers.fasta
[2023-06-29 21:39:46,698] [INFO] Task started: Blastn
[2023-06-29 21:39:46,699] [INFO] Running command: blastn -query GCA_016291815.1_ASM1629181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30c4be52-b8b3-4552-a7d6-7459b1ac4600/dqc_reference/reference_markers.fasta -out GCA_016291815.1_ASM1629181v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:39:47,302] [INFO] Task succeeded: Blastn
[2023-06-29 21:39:47,305] [INFO] Selected 38 target genomes.
[2023-06-29 21:39:47,306] [INFO] Target genome list was writen to GCA_016291815.1_ASM1629181v1_genomic.fna/target_genomes.txt
[2023-06-29 21:39:47,312] [INFO] Task started: fastANI
[2023-06-29 21:39:47,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e694151-943e-452c-a2fe-db1846793f87/GCA_016291815.1_ASM1629181v1_genomic.fna.gz --refList GCA_016291815.1_ASM1629181v1_genomic.fna/target_genomes.txt --output GCA_016291815.1_ASM1629181v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:40:11,675] [INFO] Task succeeded: fastANI
[2023-06-29 21:40:11,676] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30c4be52-b8b3-4552-a7d6-7459b1ac4600/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:40:11,676] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30c4be52-b8b3-4552-a7d6-7459b1ac4600/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:40:11,681] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:40:11,681] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:40:11,681] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	76.1521	50	648	95	below_threshold
Alistipes dispar	strain=5CPEGH6	GCA_006542685.1	2585119	2585119	type	True	75.74	51	648	95	below_threshold
Alistipes megaguti	strain=Marseille-P5997	GCA_900604385.1	2364787	2364787	type	True	75.0599	51	648	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:40:11,683] [INFO] DFAST Taxonomy check result was written to GCA_016291815.1_ASM1629181v1_genomic.fna/tc_result.tsv
[2023-06-29 21:40:11,684] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:40:11,684] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:40:11,684] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30c4be52-b8b3-4552-a7d6-7459b1ac4600/dqc_reference/checkm_data
[2023-06-29 21:40:11,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:40:11,709] [INFO] Task started: CheckM
[2023-06-29 21:40:11,709] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016291815.1_ASM1629181v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016291815.1_ASM1629181v1_genomic.fna/checkm_input GCA_016291815.1_ASM1629181v1_genomic.fna/checkm_result
[2023-06-29 21:40:45,214] [INFO] Task succeeded: CheckM
[2023-06-29 21:40:45,215] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.20%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 21:40:45,234] [INFO] ===== Completeness check finished =====
[2023-06-29 21:40:45,234] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:40:45,234] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016291815.1_ASM1629181v1_genomic.fna/markers.fasta)
[2023-06-29 21:40:45,234] [INFO] Task started: Blastn
[2023-06-29 21:40:45,234] [INFO] Running command: blastn -query GCA_016291815.1_ASM1629181v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30c4be52-b8b3-4552-a7d6-7459b1ac4600/dqc_reference/reference_markers_gtdb.fasta -out GCA_016291815.1_ASM1629181v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:40:46,196] [INFO] Task succeeded: Blastn
[2023-06-29 21:40:46,200] [INFO] Selected 29 target genomes.
[2023-06-29 21:40:46,200] [INFO] Target genome list was writen to GCA_016291815.1_ASM1629181v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:40:46,214] [INFO] Task started: fastANI
[2023-06-29 21:40:46,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e694151-943e-452c-a2fe-db1846793f87/GCA_016291815.1_ASM1629181v1_genomic.fna.gz --refList GCA_016291815.1_ASM1629181v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016291815.1_ASM1629181v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:40:57,542] [INFO] Task succeeded: fastANI
[2023-06-29 21:40:57,560] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 21:40:57,560] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_902801205.1	s__Cryptobacteroides sp902801205	92.5526	583	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.36	98.05	0.90	0.89	3	-
GCA_017477245.1	s__Cryptobacteroides sp017477245	78.2766	150	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.05	97.38	0.81	0.78	3	-
GCA_016287075.1	s__Cryptobacteroides sp016287075	78.2119	181	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316955.1	s__Cryptobacteroides sp900316955	78.0122	183	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902798975.1	s__Cryptobacteroides sp902798975	77.9604	127	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316525.1	s__Cryptobacteroides sp900316525	77.948	206	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.78	96.71	0.88	0.84	4	-
GCA_017428725.1	s__Cryptobacteroides sp017428725	77.9411	168	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.64	97.64	0.87	0.87	2	-
GCA_017438265.1	s__Cryptobacteroides sp017438265	77.916	146	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	96.23	96.11	0.87	0.85	4	-
GCA_017483985.1	s__Cryptobacteroides sp017483985	77.8211	153	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902762435.1	s__Cryptobacteroides sp902762435	77.7619	173	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.59	98.59	0.91	0.91	2	-
GCA_001602885.1	s__Cryptobacteroides sp001602885	77.7096	78	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779765.1	s__Cryptobacteroides sp902779765	77.6621	126	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.01	96.70	0.92	0.90	3	-
GCA_017469745.1	s__Cryptobacteroides sp017469745	77.662	143	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001602865.1	s__Cryptobacteroides sp001602865	77.6607	93	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234475.1	s__Cryptobacteroides sp905234475	77.6555	152	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016290835.1	s__Cryptobacteroides sp016290835	77.6492	143	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017400135.1	s__Cryptobacteroides sp017400135	77.6057	130	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789245.1	s__Cryptobacteroides sp902789245	77.5835	166	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.35	96.71	0.87	0.86	3	-
GCA_000431015.1	s__Cryptobacteroides sp000431015	77.4422	134	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.39	98.13	0.87	0.74	9	-
GCA_017458145.1	s__Cryptobacteroides sp017458145	77.4305	152	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017454905.1	s__Cryptobacteroides sp017454905	77.317	163	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017471045.1	s__Cryptobacteroides sp017471045	77.2734	137	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002438845.1	s__Cryptobacteroides sp002438845	76.9691	108	648	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.65	99.58	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-29 21:40:57,562] [INFO] GTDB search result was written to GCA_016291815.1_ASM1629181v1_genomic.fna/result_gtdb.tsv
[2023-06-29 21:40:57,563] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:40:57,572] [INFO] DFAST_QC result json was written to GCA_016291815.1_ASM1629181v1_genomic.fna/dqc_result.json
[2023-06-29 21:40:57,572] [INFO] DFAST_QC completed!
[2023-06-29 21:40:57,572] [INFO] Total running time: 0h1m23s